aRNApipe: a balanced, efficient and distributed pipeline for processing RNA-seq data in high-performance computing environments

Summary: The wide range of RNA-seq applications and their high-computational needs require the development of pipelines orchestrating the entire workflow and optimizing usage of available computational resources. We present aRNApipe, a project-oriented pipeline for processing of RNA-seq data in high-performance cluster environments. aRNApipe is highly modular and can be easily migrated to any high-performance computing (HPC) environment. The current applications included in aRNApipe combine the essential RNA-seq primary analyses, including quality control metrics, transcript alignment, count generation, transcript fusion identification, alternative splicing and sequence variant calling. aRNApipe is project-oriented and dynamic so users can easily update analyses to include or exclude samples or enable additional processing modules. Workflow parameters are easily set using a single configuration file that provides centralized tracking of all analytical processes. Finally, aRNApipe incorporates interactive web reports for sample tracking and a tool for managing the genome assemblies available to perform an analysis. Availability and documentation: https://github.com/HudsonAlpha/aRNAPipe ; DOI: 10.5281/zenodo.202950. Contact: rmyers@hudsonalpha.org. Supplementary information: Supplementary data are available at Bioinformatics online.